Normalization among samples from different sequencing runs

[christoforos-dimitropoulos]

Hello,

First of all, thanks for the amazing tool that you provide. I am currently using it to map TCRα and TCRβ sequences of sorted CD4 T cells (bulk RNA-seq) from mice, and I would like to perform a clonotypic overlap analysis of two different subsets of CD4 T cells in two different tissues.

However, my samples were sequenced in three different runs. Even though the sequencing depth looks quite similar, I was wondering what limitations this analysis might face. If there are any, what normalization/downsampling methods would you recommend?

Thanks a lot in advance,
C.